---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[14], line 1
----> 1 sdata["cell_labels"] = sd.rasterize(
...
9 )
File ~/miniconda3/envs/g3/lib/python3.11/site-packages/spatialdata/_core/operations/rasterize.py:351, in rasterize(data, axes, min_coordinate, max_coordinate, target_coordinate_system, target_unit_to_pixels, target_width, target_height, target_depth, sdata, value_key, table_name, return_regions_as_labels, agg_func, return_single_channel)
349 return rasterized
350 if model in (PointsModel, ShapesModel):
--> 351 return rasterize_shapes_points(
... 368 )
369 raise ValueError(f"Unsupported model {model}.")
File ~/miniconda3/envs/g3/lib/python3.11/site-packages/spatialdata/_core/operations/rasterize.py:723, in rasterize_shapes_points(data, axes, min_coordinate, max_coordinate, target_coordinate_system, target_unit_to_pixels, target_width, target_height, target_depth, element_name, sdata, value_key, table_name, return_regions_as_labels, agg_func, return_single_channel)
721 max_uint16 = np.iinfo(np.uint16).max
722 if max_label > max_uint16:
--> 723 raise ValueError(f"Maximum label index is {max_label}. Values higher than {max_uint16} are not supported.")
724 agg = agg.astype(np.uint16)
725 return Labels2DModel.parse(agg, transformations=transformations)
ValueError: Maximum label index is 117340. Values higher than 65535 are not supported.
import numpy as np
import spatialdata as sd
def get_n_coords(n):
coords = np.random.rand(n, 2)
return coords
sdata1 = sd.SpatialData(points={"points": PointsModel.parse(get_n_coords(65534))})
sdata2 = sd.SpatialData(points={"points": PointsModel.parse(get_n_coords(65536))})
# sdata1 would work
img_extent = sd.get_extent(sdata2['points'])
sd.rasterize(
sdata2["points"],
["x", "y"],
min_coordinate=[int(img_extent["x"][0]), int(img_extent["y"][0])],
max_coordinate=[int(img_extent["x"][1]), int(img_extent["y"][1])],
target_coordinate_system="global",
target_unit_to_pixels=1,
return_regions_as_labels=True,
)
I am using
sd.rasterizeon cell polygons of >100k cells and run into the error.--------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[14], line 1 ----> 1 sdata["cell_labels"] = sd.rasterize( ... 9 ) File ~/miniconda3/envs/g3/lib/python3.11/site-packages/spatialdata/_core/operations/rasterize.py:351, in rasterize(data, axes, min_coordinate, max_coordinate, target_coordinate_system, target_unit_to_pixels, target_width, target_height, target_depth, sdata, value_key, table_name, return_regions_as_labels, agg_func, return_single_channel) 349 return rasterized 350 if model in (PointsModel, ShapesModel): --> 351 return rasterize_shapes_points( ... 368 ) 369 raise ValueError(f"Unsupported model {model}.") File ~/miniconda3/envs/g3/lib/python3.11/site-packages/spatialdata/_core/operations/rasterize.py:723, in rasterize_shapes_points(data, axes, min_coordinate, max_coordinate, target_coordinate_system, target_unit_to_pixels, target_width, target_height, target_depth, element_name, sdata, value_key, table_name, return_regions_as_labels, agg_func, return_single_channel) 721 max_uint16 = np.iinfo(np.uint16).max 722 if max_label > max_uint16: --> 723 raise ValueError(f"Maximum label index is {max_label}. Values higher than {max_uint16} are not supported.") 724 agg = agg.astype(np.uint16) 725 return Labels2DModel.parse(agg, transformations=transformations) ValueError: Maximum label index is 117340. Values higher than 65535 are not supported.I was wondering if the threshold needs to be that low or could be increased?
To reproduce the error: